project env. setup 저장용 포스트

conda create --name Project01 python=3.10
conda activate Project01

conda install -c conda-forge hdf5
conda install -c anaconda openssl

#conda search r-base
conda install -c conda-forge r-base=4.3.1

# for Seurat v5
conda install -c conda-forge r-igraph
conda install -c conda-forge r-shiny

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")
install.packages("remotes")

install.packages("RCurl")

# Seurat v5
remotes::install_github("satijalab/seurat", "seurat5")
remotes::install_github("satijalab/seurat-data", "seurat5")
remotes::install_github("mojaveazure/seurat-object", "seurat5")
remotes::install_github("satijalab/azimuth", "seurat5")
remotes::install_github("satijalab/seurat-wrappers", "seurat5")
remotes::install_github("stuart-lab/signac", "seurat5")
remotes::install_github("bnprks/BPCells")

  libxmlsec1.so.1: cannot open shared object file: No such file or directory

# scTransform 
BiocManager::install("glmGamPoi")
install.packages("sctransform")

# Harmony
BiocManager::install("harmony")

# monocle3
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'HDF5Array',
                       'terra', 'ggrastr'))
install.packages("devtools")
devtools::install_github('cole-trapnell-lab/monocle3')

BiocManager::install("kstreet13/slingshot")

Conda env로 까는거 말안들어서 결국 GCC부터 다시깔고 R 4.3.1깔고 R-package설치했더니 잘됨..

Seurat4

conda create -n Seurat4
conda activate Seurat4

conda search r-base
conda install -c conda-forge r-base=4.3.2

conda install -c conda-forge r-devtools

# in R
# .libPaths()
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.18")

remotes::install_version(package = 'Seurat', version = package_version('4.4.0'))

install.packages("igraph")
install.packages("RANN")
install.packages("WeightedCluster")
install.packages("corpcor")
install.packages("weights")
install.packages("Hmisc")
install.packages("Matrix")
install.packages("patchwork")
install.packages("plyr")
install.packages("irlba")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")